Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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Rank Gene Hugo description Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1951 to 2000 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
Interaction Map
red
green
network_comparison
488 SART1 squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146] Divided High confidence 225.026 209.798 1.07258
TMOD4 skeletal muscle tropomodulin (sk-tmod) (tropomodulin 4). [swissprot;acc:q9nzq9] Low confidence 209.136 202.478 1.03288
489 ATG3 apg3p; pc3-96 protein. [refseq;acc:nm_022488] Subtracted High confidence 82.5916 98.0548 15.4632
PPM1B protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] Divided 231.276 215.627 1.07257
TMOD3 ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9] Low confidence 209.136 202.478 1.03288
USP22 ubiquitin carboxyl-terminal hydrolase 22 (ec 3.1.2.15) (ubiquitin thiolesterase 22) (ubiquitin-specific processing protease 22) (deubiquitinating enzyme 22) (fragment). [swissprot;acc:q9upt9] Subtracted 207.407 200.869 6.538
490 ARHGEF7 rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155] Divided High confidence 220.183 236.015 1.0719
FUCA2 fucosidase, alpha-l- 2, plasma. [refseq;acc:nm_032020] Subtracted Low confidence 202.311 195.778 6.533
SSB lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455] High confidence 242.531 227.136 15.395
TMOD1 tropomodulin 1 (erythrocyte tropomodulin) (e-tmod). [swissprot;acc:p28289] Divided Low confidence 209.136 202.478 1.03288
491 no value rna-binding protein. [refseq;acc:nm_019027] Subtracted 203.821 197.289 6.532
GTPBP4 nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4] Divided High confidence 251.83 234.951 1.07184
PITRM1 metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] Subtracted 150.959 166.351 15.392
SNX9 sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1] Divided Low confidence 209.136 202.478 1.03288
492 no value apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] Subtracted 203.821 197.291 6.53
ALG1 beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] High confidence 150.982 166.372 15.39
PAK2 serine/threonine-protein kinase pak 2 (ec 2.7.1.-) (p21-activated kinase 2) (pak-2) (pak65) (gamma-pak) (s6/h4 kinase). [swissprot;acc:q13177] Divided 220.171 235.979 1.0718
TMOD2 neuronal tropomodulin (n-tmod) (tropomodulin 2). [swissprot;acc:q9nzr1] Low confidence 209.136 202.478 1.03288
493 COG5 conserved oligomeric golgi complex subunit 5 (13s golgi transport complex 90 kda subunit) (gtc-90) (golgi transport complex 1). [swissprot;acc:q9up83] High confidence 220.172 235.98 1.0718
FUCA1 tissue alpha-l-fucosidase precursor (ec 3.2.1.51) (alpha-l-fucosidase i) (alpha-l-fucoside fucohydrolase). [swissprot;acc:p04066] Subtracted Low confidence 202.271 195.742 6.529
TNK2 activated p21cdc42hs kinase. [refseq;acc:nm_005781] Divided 209.136 202.478 1.03288
ZNRD1 zinc ribbon domain containing, 1; transcription-associated zinc ribbon protein; rna polymerase i small specific subunit rpa12. [refseq;acc:nm_014596] Subtracted High confidence 236.751 252.038 15.287
494 EEF1B2 elongation factor 1-beta (ef-1-beta). [swissprot;acc:p24534] Divided Low confidence 206.154 199.596 1.03286
EIF5 eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] Subtracted 208.004 201.497 6.507
MTX2 metaxin 2. [swissprot;acc:o75431] High confidence 219.537 234.793 15.256
PAK1 serine/threonine-protein kinase pak 1 (ec 2.7.1.-) (p21-activated kinase 1) (pak-1) (p65-pak) (alpha-pak). [swissprot;acc:q13153] Divided 220.172 235.98 1.0718
495 no value splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] Subtracted Low confidence 198.464 191.96 6.504
LIMD1 lim domains containing 1. [refseq;acc:nm_014240] Divided 203.117 196.671 1.03278
PAK3 serine/threonine-protein kinase pak 3 (ec 2.7.1.-) (p21-activated kinase 3) (pak-3) (beta-pak) (oligophrenin-3). [swissprot;acc:o75914] High confidence 220.171 235.979 1.0718
YME1L1 yme1-like 1 isoform 3; atp-dependent metalloprotease ftsh1 homolog. [refseq;acc:nm_014263] Subtracted 222.146 237.393 15.247
496 no value dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9] 235.18 250.419 15.239
probable mitochondrial import receptor subunit tom7 homolog (translocase of outer membrane 7 kda subunit homolog) (protein ad- 014). [swissprot;acc:q9p0u1] Divided Low confidence 203.117 196.671 1.03278
PPAN-P2RY11 suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] High confidence 250.938 234.134 1.07177
RNF113A zinc finger protein 183. [swissprot;acc:o15541] Subtracted Low confidence 205.192 198.726 6.466
497 CAPS calcyphosine. [swissprot;acc:q13938] 204.363 197.899 6.464
EBNA1BP2 probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] Divided High confidence 251.344 234.514 1.07177
SART1 squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146] Subtracted 225.026 209.798 15.228
SF4 splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] Divided Low confidence 203.117 196.671 1.03278
498 ARHGEF6 rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052] High confidence 220.161 235.95 1.07172
KIFAP3 kinesin-associated protein 3 (smg gds-associated protein). [swissprot;acc:q92845] Low confidence 203.117 196.671 1.03278
RCL1 rna 3'-terminal phosphate cyclase-like protein (hspc338). [swissprot;acc:q9y2p8] Subtracted 203.85 197.403 6.447
TLX3 t-cell leukemia homeobox protein 3 (homeobox protein hox-11l2). [swissprot;acc:o43711] High confidence 237.28 252.492 15.212
499 BARX1 homeobox protein barh-like 1. [swissprot;acc:q9hbu1]
LIMD1 lim domains containing 1. [refseq;acc:nm_014240] Low confidence 203.117 196.671 6.446
POLI polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] Divided 203.167 196.732 1.03271
TPI1 triosephosphate isomerase (ec 5.3.1.1) (tim). [swissprot;acc:p00938] High confidence 231.496 248.048 1.0715
500 no value probable mitochondrial import receptor subunit tom7 homolog (translocase of outer membrane 7 kda subunit homolog) (protein ad- 014). [swissprot;acc:q9p0u1] Subtracted Low confidence 203.117 196.671 6.446
ING2 inhibitor of growth family, member 1-like; inhibitor of growth 1-like. [refseq;acc:nm_001564] Divided High confidence 224.662 240.673 1.07127
OPN4 opsin 4 (melanopsin). [swissprot;acc:q9uhm6] Subtracted 237.28 252.492 15.212
RCL1 rna 3'-terminal phosphate cyclase-like protein (hspc338). [swissprot;acc:q9y2p8] Divided Low confidence 203.85 197.403 1.03266

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Hugo is the HGNC identifier if it exists
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.
- http://analysis.yellowcouch.org/